Virtual BiodiversityViBRANT
SEVENTH FRAMEWORK PROGRAMME -infrastructure
Community web sites: small pieces loosely joinedDave Roberts, Simon Rycroft & Vince Smith
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Small pieces loosely joined Has many potential meanings:
Joining contributors together to form communities
Joining the data together that go towards forming a Scratchpad
Joining Scratchpad content with the landscape of biodiversity informatics data on the web
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Goal ...
Data set ...
People ...
Addressing the challenges of taxonomy
Inventory the Earth’s speciesDocument their relationships“Publish” & apply these data
1.8 M described spp. (10M names)300M pages (over last 250 years)1.5-3B specimens
4-6,000 taxonomists30-40,000 “pro-amateurs”Many more citizen scientists?
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Magic
Your data Your web site
A website for you & your community
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Dynamic web pages
Taxonomy import, management and navigation
Reference manager / Endnote support for bibliographies
Image galleries, image upload & annotation
Nexus / Newick import for visualising phylogenies
Character matricies (discrete, morphometric and text characters)
Presence / absence country maps
Specimen & location records (DwC)
Newsletters & Web fora with e-mail integration
User blogs
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Import from CSV text file to any content type
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Taxonomy & LiteratureLice, mosquitos, freeloader flies, ...
(rapid upload and management of names, synonyms & bibliographic data)
Freeloader Flies, fungus gnats, ...(publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life)
Taxon descriptions & Publications
European Mosquito Bulletin, Phasmid Studies, ...(submission, review & dissemination of articles)
eJournals
Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps)
Characters, Phylogeny & Specimens
Image GalleriesDragon trees, nanno fossils, cockroaches, fungi, polychaetes, ...
(rapid upload, annotation & display of images)
ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ...(space for data collection, services, discussion & organisation)
Societies, Organisations & Projects
240
200
160
120
80
40
0
Year 1 Year 2 Year 3 Year 4
3000
2500
2000
1500
1000
500
0
Registered UsersSites
SitesUsers
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
A Virtual Research Environment (Scratchpads)where users can safely store, share and manage their research information.
Analytical servicesfor users to build identification keys and phylogenetic trees.
A publication platformfor users to compile taxonomic manuscripts automatically from their site.
A portalfor users to access public biodiversity research information and literature.
Training, support & sociological studyhelping research communities to use these tools and services.
A standards compliant technical architecturethat can be sustained by biodiversity research community.
ViBRANT Products
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
ScratchpadsVirtual Research
EnvironmentPhylogenetic
analysisBioclimaticmodelling& metrics
Identificationtools
Matrix dataeditor
Biodiversity data
publishingScholarlymanuscriptpublishing
DistributedScratchpad
hostingSoftwaremodule
integration
Sustainabilityplan
Communalbiodiversity
literature
Biodiversityliteraturemarkup
Biodiversitydatamining
Citizenscience
programme
Fieldrecordingsupport
Usersociology
study
Userfeedbacksystems
Training& outreachprogramme
Biodiversitydata
standards
Dataaggregation
portal
GBIFintegrationactivities
Biodiversityvisualisation
layers
Controlledvocabulary
platformNetworking
WP3. TrainingWP4. Standards
WP8. Mobilisation
ResearchWP2. ArchitectureWP7. Literature
ServiceWP5. Data
WP6. Publishing
The “chromosome”
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
ScratchpadsVirtual Research
EnvironmentPhylogenetic
analysisBioclimaticmodelling& metrics
Identificationtools
Matrix dataeditor
Biodiversitydata
publishingScholarlymanuscriptpublishing
DistributedScratchpad
hostingSoftwaremodule
integration
Sustainabilityplan
Communalbiodiversity
literature
Biodiversityliteraturemarkup
Biodiversitydatamining
Citizenscience
programme
Fieldrecordingsupport
Usersociology
study
Userfeedbacksystems
Training& outreachprogramme
Biodiversitydata
standards
Dataaggregation
portal
GBIFintegrationactivities
Biodiversityvisualisation
layers
Controlledvocabulary
platformNetworking
WP3. TrainingWP4. Standards
WP8. Mobilisation
ResearchWP2. ArchitectureWP7. Literature
ServiceWP5. Data
WP6. Publishing
GBIF
GBIF
GBIF
GBIF
GBIF
The “chromosome”
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
More reliable (e.g., distribute the servers)More functional (e.g., phylogenetic & publication services) Easier to use (better workflows)Prettier (better graphical design - more intuitive)More integrated (for data stored inside & outside the Scratchpad framework)More sustainable (simple administration, distribute developers, development sandbox)
“making the Scratchpads better”
“making natural history better”Easier to compile, manage and reuse your dataEasier to find and reuse other peoples data Promoting your data inside & outside the taxonomic communityGetting people to work for you (crowdsourcing)
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Manuscript preparation on a Scratchpad
Submit as XML
Produce PDF
Enhanced XML
Register with ZooBank,
GBIF, EoL etc.
Printed paper
Enhanced HTML
Send to reviewers
AuthorAuthor
Publisher
Public
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
https://git.scratchpads.eu/viewgit
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Thank you for your attention.
Any questions
http://vbrant.eu http://scratchpads.eu
e-mail: [email protected]